Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011968.1 Corchorus capsularis cultivar CVL-1 contig11989, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7582
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:985 original size:333 final size:332
Alignment explanation
Indices: 3--2607 Score: 3469
Period size: 333 Copynumber: 7.8 Consensus size: 332
1 AA
* * * * * *
3 CATCATAATCGAATTTCGATTTAATTAGAAATTAATTCGTAAAAAATAGGAAAAACGATTTTAGA
1 CATCAGAATCGAGTTTCGATTTAAGTAGAAATTAATTCG-AAAAAATAAGAAAAACAATATTAGA
* * * * * * *** * *
68 AACATGAAAA-ACCATCCAATATTTATGATGTTGAATTATATATTTTTTTATGAATATTGTGGCT
65 AGCGTGAAAATCCCTTCAAAT-TTTTTGGCATTGAATTATATA-TTATTTATGAGTATTGTGGCT
* * * *
132 AAAAATTGAGGAAAAATTTTTCGGCTCAATTTTTGCAAAATTTTAGCCGAAATGGTGTACTAACA
128 AAAAATTGAGGAAAAATTTTTCGGGTAAATTTTTGCAAAATTTCAGCCGAAATCGTGTACT---A
* ** * * * * * *
197 ACCATCACG-GTTTTCAGCCAAAAAAGTGTTCCAGGAACCCGACTCAATTTTGCATTATTTTTAG
190 ACCATCACGATTTTTTGGCTAAAAACGCGTTCCGGGAACCCGACTCAATTTTGCATGATTTTTGG
* * * * * * * *
261 TGCTATCACTGCTTGAAATATATGCTTT-AATATAACCAAATCACTGCCACATTGGACTTCAGGA
255 CGCCATGACTCCTTGAAATATCTG-TTTCAATCTAACCAAATCTCTGCCACATTGGACTTAAGGA
325 TTT-T-TTTATGAG
319 TTTGTGTTTATGAG
* * * * *
337 CATTAGAAACGAGTTTCGATTTAAGAAGAAATTAATTCGGAAAAGAAAGAAAAAGAAAAAAAATA
1 CATCAGAATCGAGTTTCGATTTAAGTAGAAATTAATTC-G---A-AAA-AATAAGAAAAACAATA
* * * * *
402 TTAGAAACGTGAAAAGCCCTTC-AATTTTTTGGTATTGAATTATATATTCTTTATGAGTATTGAG
60 TTAGAAGCGTGAAAATCCCTTCAAATTTTTTGGCATTGAATTATATATTATTTATGAGTATTGTG
* * * **
466 GCAAAAAATTGAGGAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAATCGAAATCGTGTACTA
125 GCTAAAAATTGAGGAAAAATTTTTCGGGTAAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTA
* *
531 ACCATCACGGTTTTTTGGCTAAAAACGCGTTCCGGGAACCCGACTCAATTTTGCATGATTTTTGA
190 ACCATCACGATTTTTTGGCTAAAAACGCGTTCCGGGAACCCGACTCAATTTTGCATGATTTTTGG
* * *
596 TGCCATGACTCCTTGAAATATATGTTTCAATCTAACCAAATCTCTGCCACATTGGACTTAAAGAT
255 CGCCATGACTCCTTGAAATATCTGTTTCAATCTAACCAAATCTCTGCCACATTGGACTTAAGGAT
*
661 TTGTGTTTACGAG
320 TTGTGTTTATGAG
*
674 CATCATAATCGAGTTTCGATTTAAGTAGAAATTAATTCGAAAAAATAAGAAAAACAATATTAGAA
1 CATCAGAATCGAGTTTCGATTTAAGTAGAAATTAATTCGAAAAAATAAGAAAAACAATATTAGAA
* * *
739 GCGTGAAAATCCCTTTAAATTTTTTGGCATTCAATTATATATTGTTTATGAGTATTGTGGCTAAA
66 GCGTGAAAATCCCTTCAAATTTTTTGGCATTGAATTATATATTATTTATGAGTATTGTGGCTAAA
* * *
804 AATTGAGGAAAAATTTTTCGGGTAAATTTTT-CAAAACTTCAACCCAAATCGTGTACTAACCATC
131 AATTGAGGAAAAATTTTTCGGGTAAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTAACCATC
* * * *
868 ACGATTTTTTTTGGCTAAAAACGCGTTTCGGGAATCCGACTCAATTTTGCATGATTTCTGTCGCC
196 ACGA--TTTTTTGGCTAAAAACGCGTTCCGGGAACCCGACTCAATTTTGCATGATTTTTGGCGCC
* * * * * * * *
933 ATTACACCTTGAAATATCTATTTTAATCTAACCGAATCACTGCCAAATTGGACTTAAAGATTTGT
259 ATGACTCCTTGAAATATCTGTTTCAATCTAACCAAATCTCTGCCACATTGGACTTAAGGATTTGT
* *
998 TTTTACGAG
324 GTTTATGAG
* * *
1007 CATCAGAATCGAGTTTCGATTTAAGAAGAAATTAATTCGAAAAAAAAAG-AAAACAATATTATAA
1 CATCAGAATCGAGTTTCGATTTAAGTAGAAATTAATTCGAAAAAATAAGAAAAACAATATTAGAA
* * * * * * * *
1071 GCGTGAAAAACCCTTCAATTTTTTTGGTACTAAATTATATATTATTTACGAGTATTATGGCAAAA
66 GCGTGAAAATCCCTTCAAATTTTTTGGCATTGAATTATATATTATTTATGAGTATTGTGGCTAAA
* * * * * * *
1136 AATCGAGGAAAAATTTTCCTGGTCAAGTTTTGCAAAATTTCAGCCTAAATCGTG---T-A-CGTC
131 AATTGAGGAAAAATTTTTCGGGTAAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTAACCATC
*
1196 ACGATTTTTTCGCTAAAAACGCGTTCCGGGAACCCGACTCAATTTTGCATGATTTTTGGCGCCAT
196 ACGATTTTTTGGCTAAAAACGCGTTCCGGGAACCCGACTCAATTTTGCATGATTTTTGGCGCCAT
* * *
1261 GACTCCTTGAAATATCTGTTTCAATCTAATCAAATCTCTGCCAGATTGGATTTAAGGATTTGTGT
261 GACTCCTTGAAATATCTGTTTCAATCTAACCAAATCTCTGCCACATTGGACTTAAGGATTTGTGT
*
1326 TTATAAG
326 TTATGAG
1333 CATCAGAATCGAGTTTCGATTTAAGTAGAAATTAATTCGAAAAAATAAGAAAAACAATATTAGAA
1 CATCAGAATCGAGTTTCGATTTAAGTAGAAATTAATTCGAAAAAATAAGAAAAACAATATTAGAA
* *
1398 GCGTGAAAATCCCTTCAATTTTTTTGGCATTGAATTATATATTATATTATGAGTATTGTGGCTTA
66 GCGTGAAAATCCCTTCAAATTTTTTGGCATTGAATTATATATTAT-TTATGAGTATTGTGGCTAA
* * *
1463 AAATTGAGGAAAAATTTTTCTGGTAAATTTTTGCAAAATTTCAGCCTAAATCGTGTAATAACCAT
130 AAATTGAGGAAAAATTTTTCGGGTAAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTAACCAT
1528 CACGATTTTTTGGCTAAAAACGCGTTCCGGGAACCCGACTCAATTTTGCATGATTTTTGGCGCCA
195 CACGATTTTTTGGCTAAAAACGCGTTCCGGGAACCCGACTCAATTTTGCATGATTTTTGGCGCCA
* *
1593 TGACTCCTTGAAATATCTGTTTCAATCTAACCAAATCTCTGCCAGATTGGATTTAAGGATTTGTG
260 TGACTCCTTGAAATATCTGTTTCAATCTAACCAAATCTCTGCCACATTGGACTTAAGGATTTGTG
*
1658 TTTATAAG
325 TTTATGAG
1666 CATCAGAATCGAGTTTCGATTTAAGTAGAAATTAATTCGAAAAAATAAGAAAAACAATATTAGAA
1 CATCAGAATCGAGTTTCGATTTAAGTAGAAATTAATTCGAAAAAATAAGAAAAACAATATTAGAA
* * * * *
1731 GCGTGAAAAT-CCTGTCAATTTTTTTGGCATTGAATTATATATTCTATTCTGAGTATTATGGCTT
66 GCGTGAAAATCCCT-TCAAATTTTTTGGCATTGAATTATATATTAT-TTATGAGTATTGTGGCTA
* * * *
1795 AAAATTGAGGAAAAAAATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATTGTGTACTAACC
129 AAAATTGAGG-AAAAATTTTTCGGGTAAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTAACC
* ** *
1860 ATCACGATTTTTTGGCGAAAAACGATTTTCGGGAA-CCGACTCAATTTTGCATGATTTTTGGCGC
193 ATCACGATTTTTTGGCTAAAAACGCGTTCCGGGAACCCGACTCAATTTTGCATGATTTTTGGCGC
* *
1924 CATGACTCCTTGAAATATCTATTTTAATCTAACCAAATCTCTGCCACATTGGACTTAAGGATTTG
258 CATGACTCCTTGAAATATCTGTTTCAATCTAACCAAATCTCTGCCACATTGGACTTAAGGATTTG
* *
1989 TTTTTACGAG
323 TGTTTATGAG
* *
1999 CATCAGAATCGAGTTTCGATTTAAGAAGAAATTAATTCGAAAAAAAAAAGAAAAACAATATTAGA
1 CATCAGAATCGAGTTTCGATTTAAGTAGAAATTAATTCG-AAAAAATAAGAAAAACAATATTAGA
* * * **
2064 AGCGTGAAAATCCCTTCAATTTTTTTGGTATTGAATTATATATTATTTACGAGTATTGTGGGAAA
65 AGCGTGAAAATCCCTTCAAATTTTTTGGCATTGAATTATATATTATTTATGAGTATTGTGGCTAA
* * * * *
2129 AAAATGAGGAAAAATTTTTCAGGTAAATTTTTACAAAATATCAGCCTAAATCGTGTACTAACCAT
130 AAATTGAGGAAAAATTTTTCGGGTAAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTAACCAT
* * *
2194 CACGATTTTTTGGCTAAAAACACGTTCCGGGAACCCAACTCAATTTTGCGTGATTTTTGGCGCCA
195 CACGATTTTTTGGCTAAAAACGCGTTCCGGGAACCCGACTCAATTTTGCATGATTTTTGGCGCCA
* * *
2259 TGACTCCTTGAAATATCTGTTTGAATCTAACCAAATCTCTGCCAGATTGGATTTAAGGATTTGTG
260 TGACTCCTTGAAATATCTGTTTCAATCTAACCAAATCTCTGCCACATTGGACTTAAGGATTTGTG
*
2324 TTTATAAG
325 TTTATGAG
2332 CATCAGAATCGAGTTTCGATTTAAGTAGAAATTAATTCGAAAAAATAAGAAAAACAATATTAGAA
1 CATCAGAATCGAGTTTCGATTTAAGTAGAAATTAATTCGAAAAAATAAGAAAAACAATATTAGAA
* * * *
2397 GCGTGAAAATCCCTTC-AATTTTTTGGCATTGAATTATATATTCTATTCTGAGTATTATGGCTTA
66 GCGTGAAAATCCCTTCAAATTTTTTGGCATTGAATTATATATTAT-TTATGAGTATTGTGGCTAA
* * * *
2461 AAATTGAGGAAAAAATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATTGTGTACTAACCAT
130 AAATTGAGGAAAAATTTTTCGGGTAAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTAACCAT
* ** *
2526 CACGATTTTTTGGCGAAAAACGATTTTCGGGAACCCGACTCAATTTTGCATGATTTTTGGCGCCA
195 CACGATTTTTTGGCTAAAAACGCGTTCCGGGAACCCGACTCAATTTTGCATGATTTTTGGCGCCA
*
2591 TTACTCCTTGAAATATC
260 TGACTCCTTGAAATATC
2608 ATTCCGACCT
Statistics
Matches: 2025, Mismatches: 219, Indels: 56
0.88 0.10 0.02
Matches are distributed among these distances:
326 162 0.08
327 55 0.03
328 73 0.04
329 1 0.00
330 1 0.00
331 91 0.04
332 435 0.21
333 744 0.37
334 187 0.09
335 105 0.05
336 2 0.00
337 116 0.06
338 21 0.01
339 28 0.01
340 4 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (332 bp):
CATCAGAATCGAGTTTCGATTTAAGTAGAAATTAATTCGAAAAAATAAGAAAAACAATATTAGAA
GCGTGAAAATCCCTTCAAATTTTTTGGCATTGAATTATATATTATTTATGAGTATTGTGGCTAAA
AATTGAGGAAAAATTTTTCGGGTAAATTTTTGCAAAATTTCAGCCGAAATCGTGTACTAACCATC
ACGATTTTTTGGCTAAAAACGCGTTCCGGGAACCCGACTCAATTTTGCATGATTTTTGGCGCCAT
GACTCCTTGAAATATCTGTTTCAATCTAACCAAATCTCTGCCACATTGGACTTAAGGATTTGTGT
TTATGAG
Found at i:4355 original size:2 final size:2
Alignment explanation
Indices: 4348--4381 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4338 TTTTTAAGTC
* *
4348 AT AT AT AT AT AT AT AT AT AC AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4382 TAATTTACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4793 original size:2 final size:2
Alignment explanation
Indices: 4786--4815 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4776 CTATTTATCA
4786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4816 TTCTGATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5651 original size:2 final size:2
Alignment explanation
Indices: 5639--5671 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5629 GTTAGGTTCG
*
5639 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5672 TTCAAAGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7377 original size:2 final size:2
Alignment explanation
Indices: 7372--7398 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7362 TTTTCATAAC
7372 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
7399 CTAGATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.